Introducing Objects into Relational Databases
Jörn Vorwald & Steffen FlemmingInstitute of Plant Genetics and Crop Plant Research
GaterslebenCorrensstraße 3, D-06466 Gatersleben,
http://www.ipk-gatersleben.de, [email protected]
Introduction
While modeling a new information system for the gene bank of the Institute of Plant Genetics and Crop Plant Research, Gatersleben (IPK), the idea of introducing object oriented concepts into the database model focussing the requirements of gene bank germplasm and data management came up. As a result, a sophisticated model of objects handled by the information system has been introduced into the model. Even if these concepts will not be introduced into the GBIS* database due to non-technical reasons, the approach seemed to be helpful for other databases or information systems to handle complexity and to avoid disadvantages of the relational paradigm.In the following presentation, the evolution of objects in GBIS will be described by example and in general.Huldén (2003) introduced a parallel development of a generic concept for multiple used entities into plant genetic resources community. Our approach has been developed since 2002 and became much more excessive.
* GBIS = Gene Bank Information System
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Institutions, phase 1
Institution
splitted_into
merged_to
(collecting)Expedition
Project/Experiment
Person
structures_in
employs
leads
leads
participates_in
participates_in is_a
structures_in
• Identifying forms of institutions or related objects
• Identifying self reflecting relationships of objects• Identifying relationships between objects
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
• Replacing (multiple) relationships between objects by special „is A“ relationships• Recreating former relationships between objects as self reflecting relationship of root object
Institution
splitted_into
merged_to
(collecting)Expedition
Project/Experiment
Person
structures_in
employs
leads
leads
participates_in
participates_in is_a
structures_inis_a
is_aemploysleads participates_in
Institutions, phase 2
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Role
Institution
institutionId
Role roleIdroleroleGermanroleRemark
*
validityStartvalidityEndvalidityRemark
to*
*
• Abstracting all self reflecting relationships• Generating database model
Institution
splitted_into
merged_to
structures_in
employsleads participates_in
Institutions, phase 3
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Identifying all types of institutions or objects can be handled as institutions in the context of interest (here: managing plant genetic resources)
•Person• User• User group• Project
• Experiment• Collecting expedition• Specimen collection• (Germplasm) Core collection• International crop database
• Institution sensu stricto• Research institute
• IPK department• Botanical garden
• Gene bank• IPK curator group
• Breeder• Governmental agency• Non-governmental organisation
Institutions, phase 4
•Person• User• User group• Project• Experiment• Collecting expedition• Specimen collection• (Germplasm) Core collection• International crop database• Institution sensu stricto• Research institute• IPK department• Botanical garden• Gene bank• IPK curator group• Breeder• Governmental agency• Non-governmental organisation
Identifying a hierarchy
Generating a database representation of the hierarchy
Institution
institutionId
Role
*
to*
*
patternIdpatternpatternGermanpatternRemark
Pattern1
isOf*
*has
1
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Identifying all types of relationships of interest between institutions
Institutions, phase 5
• ((person) v (institution s. str.)) leads (project)• (person) heads (institution s. str.)• (institution s. str.) subdivides into (person)• (user group) subdivides into (user)• (project) subdivides into ((person) v (institution s. str.))• (institution) devided into (institution)• (institution) merged to (institution)• ((institution s. str.) v (person)) carries out (experiment)• (person) is responsible partner for ((collecting expedition) v (experiment))• ((institution s. str.) v (person)) maintains ((specimen collection) v (international crop database))
*syntax: (parent) role (child) | valid for all sub-patternsv represents logical ‚or‘^ represents logical ‚and‘
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
*
Identifying other main patterns within the model
Abstraction, phase 1
• (Germplasm) accessions• Samples (as materialisation of accessions)• Specimens (as materialisation of accessions and non-accessions)• Harvests• Cultivations• Sites (as geographical super-class)• Publications• Pictures• Observation acts• Descriptors• Registers• Transactions
Object
SampleAccession
Specimen
Site
isAn
1
1
Institution
Register
PicturePublication
CultivationHarvest ObservationActTransaction
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
isAn
1
1
Descriptor
isAn
1
1
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Generating a database schema on objects
Abstraction, phase 2
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Institution
institutionId
Role
*
to*
*
patternIdpatternpatternGermanpatternRemark
Pattern1
isOf*
*has
1
Object
objectId
Role
*
to*
*
patternIdpatternpatternGermanpatternRemark
Pattern1
isOf*
*has
1
Identifying other sub-patterns within the model I
Abstraction, phase 3
• Accessions• Regular accession• Potential accession• Other accession
• Samples• Seed sample• In vitro sample• Cryo sample• Vegetative sample
• Root• Bulbil• Tuber
• Specimens • Spike• Wet preparation• Seed/fruit specimen• Herbarium specimen
• Complete Plant
• Publications• Journal paper• Monograph• Book paper• Edited book• Informal paper
•Pictures• Drawing• Photo
• Colour Photo• Colour Slide
• Digital Photo• Scan
• Monochrome• Slide
• Observation acts• Descriptors
• Seedling I• Seedling II• Leaf• Floret• Cotyledon• Stand of fruit
• Harvests• Cultivations• Sites
• Diversity area• Continent
• Continental region• Country
• Region• Collecting site
• Federal state• County• > Township• >> Cultivation site
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Abstraction, phase 3
• Registers• List
• Collecting list• Sowing list
• Spring list• Autumn list
• Safety duplicate sample box• Scoring schema
• Document• Formal document
• Phytosanitary certificate• Material transfer agreement
• Informal document• Worksheet
• Request• Order request• Delivery request
• (Management) Book• Entry book• Field book• Group book• Ancestry book
•Register card• Cultivation register• Main register• Botanical register• Cultivar register
• Transactions• Order• Delivery
• Material transaction• Safety duplicate transaction• Information transaction• Specimen transaction
Identifying other sub-patterns within the model II
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Identifying all types of relationships of interest between all objects I
Abstraction, phase 4
• (sample) bears (sample)• (picture) illustrates ((accession) v (sample) v (specimen) v (institution) v (site))• (specimen) cirumstantiates (accession)• (institution) publishes (publication)• ((institution s. str.) v (person) v (collecting expedition)) collected at (collecting site)• (institution s. str.) creates (formal document)• ((institution s. str.) v (person) v (collecting expedition)) creates (collecting list)• (accession) originally materialised in (sample)• (accession) materialised in (sample)• ((institution s. str.) v (person)) borrows (specimen)• (publication) informs of ((project) v (accession) v (sample) v (specimen) v (collecting site))• (digital photo) copies ((picture) v (register))• (site) structures in (site)• (list) lists ((accession) v (sample) v (institution) v (specimen) v (picture) v (list))• (publication) contains (picture)• ((institution s. str.) v (person)) situated in (country)• (experiment) observed at (cultivation site)• (institutions s. str.) keeps (specimen)• ((book) v (worksheet)) documents (sample)• (worksheet) logs (experiment)
*syntax: (parent) role (child) | valid for all sub-patternsv represents logical ‚or‘^ represents logical ‚and‘
*
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Identifying all types of relationships of interest between all objects II
Abstraction, phase 4
• (phytosanitary certificate) attests ((accession v (sample))• (site) is country of origin of ((accession) v (specimen))• (site) is collecting site of ((accession) v (specimen))• (site) is diversity area of (accession)• (accession) splitted into (accession)• (sample) splitted into (sample)• (experiment) tests ((accession) v (sample))• (register card) registers ((accession) v (harvest) v (cultivation))• (gene bank) holds (accession)• (specimen collection) extracted (specimen)• ((institution s. str.) v (person) v (collecting expedition)) collected ((accession) v (specimen))• ((institution s. str.) v (person)) donated (accession)• (accession) is duplicate of (accession)• (institution) administers ((core collection) v (international crop database))• ((institution s. str.) v (person)) bred (accession)• (IPK curator group) manages (accession)• (user) creates (list)• (experiment) implements (scoring schema)
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Results
Summary
• generic solution for handling multiple relationships between database entities• 13 main patterns of objects with 76 sub-patterns of several levels within the hierarchy identified as important for IPK‘s germplasm information system GBIS• 46 types of relationships between the main or sub-patterns identified
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
• central administration of all objects and their relationships, e. g. for barcode based identifications• avoiding trigger based constructions in relational schemas, e. g. arcs• extensibility of concept: easy introduction of new objects and relationships to other objects into database schema
Advantages
Disadvantages
• join of role table for correct identification of kind of relationship between objects • rapid increase of object_to_object-table
• solution: indexing and partitioning• additional join of pattern table
• solution: direct join of tables of inherited objects with object_to_object-table
Acknowledgement and Reference
We thank all our colleagues for helpful discussions, namely Dr. Helmut Knüpffer and Stephan Weise from IPK, Dr. Theo van Hintum and Frank Menting from the Centre for Genetic Recources The Netherlands (CGN).
Jörn Vorwald & Steffen Flemming: Introducing Objects into Relational Databases
Huldén, M. (2003): Data abstraction models for PGR databases. Presentation on EPGRIS final conference: PGR documentation and information in Europe – towards a sustainable and user-oriented information infrastructure, 11-13 September, Prague, Czech Republic.
The project „Establishment of a central federal ex situ genebank for agricultural and horticultural crop plants: Fusion of genebanks of IPK and BAZ Braunschweig“ is kindly sponsored by the German Federal Ministry of Education and Research (BMBF).
